Merge branch 'main' of https://github.com/PAMGuard/PAMGuard.git into pr/10

.classpath

@@ -8,7 +8,6 @@
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
-			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>

.project

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>PamGuard Working</name>
+	<name>PamGuard Main</name>
 	<comment></comment>
 	<projects>
 	</projects>

buildconfigurations/Build PAMGuard.launch

@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.m2e.Maven2LaunchConfigurationType">
+    <booleanAttribute key="M2_DEBUG_OUTPUT" value="false"/>
+    <stringAttribute key="M2_GOALS" value="package shade:shade"/>
+    <booleanAttribute key="M2_NON_RECURSIVE" value="false"/>
+    <booleanAttribute key="M2_OFFLINE" value="false"/>
+    <stringAttribute key="M2_PROFILES" value=""/>
+    <listAttribute key="M2_PROPERTIES"/>
+    <stringAttribute key="M2_RUNTIME" value="EMBEDDED"/>
+    <booleanAttribute key="M2_SKIP_TESTS" value="true"/>
+    <intAttribute key="M2_THREADS" value="1"/>
+    <booleanAttribute key="M2_UPDATE_SNAPSHOTS" value="false"/>
+    <stringAttribute key="M2_USER_SETTINGS" value=""/>
+    <booleanAttribute key="M2_WORKSPACE_RESOLUTION" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
+    <stringAttribute key="org.eclipse.jdt.launching.JRE_CONTAINER" value="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-13/"/>
+    <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-mx6000m&#13;&#10;-Djava.library.path=lib64"/>
+    <stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:/PamGuard Main}"/>
+</launchConfiguration>

buildconfigurations/readme.txt

@@ -0,0 +1,16 @@
+To build an executable jar file from the PAMGuard source using Eclipse, you need to use this build configuration
+'Build PAMGuard.launch'
+You cannot simply export the project as a runnable jar file, or you will not get the required Maven dependencies. 
+To use this with Eclipse, from your workspace, select File, then import, then in the list of things to be imported select 
+Run/Debug Launch Configurations, hit Next
+Then in the Import Launch Configurations panel, browse to this folder. Select the folder (not a specific file)
+then in the left panel, select the folder, then in the right panel the configuration you wish to import 
+(i.e. Build PAMGuard.launch) and hit Finish
+Then go to 'Run Configurations' and find the launch in the 'Maven Builds' section. You'll probably have to change the 
+Base directory at the top of the panel to select the right project within your workspace. 
+Once that's done, you can Run the configuration. It will take a while to get all the Maven dependencies and will output 
+a runnable jar file into the 'targets' folder in your workspace. 
+The name and version number of the created files are taken from the POM.xml file, so edit that if you want a different name.
+For unknown reasons, it makes three files. They are all the same, you can delete the ones starting with 'original-' and 
+ending with '-shared'
+

dependency-reduced-pom.xml

@@ -2,9 +2,9 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
-  <artifactId>PamguardBeta</artifactId>
+  <artifactId>Pamguard</artifactId>
   <name>Pamguard Java12+</name>
-  <version>2.02.02</version>
+  <version>2.02.03a</version>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
   <url>www.pamguard.org</url>
   <organization>
@@ -191,11 +191,6 @@
       <id>central</id>
       <url>https://repo1.maven.org/maven2</url>
     </repository>
-    <repository>
-      <snapshots />
-      <id>github</id>
-      <url>https://maven.pkg.github.com/macster110/jpam</url>
-    </repository>
   </repositories>
   <reporting>
     <plugins>

pom.xml

@@ -3,8 +3,8 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.pamguard</groupId>
-  <artifactId>PamguardBeta</artifactId>
-  <version>2.02.02</version>
+  <artifactId>Pamguard</artifactId>
+  <version>2.02.03a</version>
   <name>Pamguard Java12+</name>
   <description>Pamguard for Java 12+, using Maven to control dependcies</description>
 	<url>www.pamguard.org</url>
@@ -318,7 +318,7 @@
 	<dependency>
 		<groupId>io.github.macster110</groupId>
 		<artifactId>jpamutils</artifactId>
-		<version>0.0.55</version>
+		<version>0.0.56</version>
 	</dependency>
 
 	<!--jpam project - Deep learning java library 
@@ -329,7 +329,7 @@
 	<dependency>
 		<groupId>io.github.macster110</groupId>
 		<artifactId>jdl4pam</artifactId>
-		<version>0.0.92</version>
+		<version>0.0.93</version>
 	</dependency> 
 			
 	<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->

src/Acquisition/FolderInputSystem.java

@@ -558,23 +558,35 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings{
 		boolean ans = false;
 		if (folderInputParameters.mergeFiles == false) return false;
 		
-		long fileEndTime = 0;
-		if (++currentFile < allFiles.size()) {
+		
+		long currFileStart = 0;
+		long currFileLength = 0;
+		long currFileEnd = 0;
 		if (currentFile >= 0) {
+			try {
 			WavFileType currentWav = allFiles.get(currentFile);
-				fileEndTime = getFileStartTime(currentWav.getAbsoluteFile());
-				fileEndTime += currentWav.getDurationInSeconds()* 1000.;
+			currFileStart = getFileStartTime(currentWav.getAbsoluteFile());
+			if (audioStream != null) {
+				fileSamples = audioStream.getFrameLength();
+				currFileLength = (long) (fileSamples * 1000 / audioStream.getFormat().getFrameRate());
+				currFileEnd = currFileStart + currFileLength;
 			}
-			else {
+			}
+			catch (Exception e) {
+				
+			}
+		}
+		if (currFileEnd == 0) {
 			//			System.out.println("OpenNextfile " + currentFile + " " + allFiles.get(currentFile).getName());
 			// also check to see if the start time of the next file is the same as the 
 			// end time of the current file.
-				fileEndTime = PamCalendar.getTimeInMillis();
+			currFileEnd = PamCalendar.getTimeInMillis();
 			long lastBit = (long) ((blockSamples * 1000L) / getSampleRate());
-				fileEndTime += lastBit;
+			currFileEnd += lastBit;
 		}
+		if (++currentFile < allFiles.size()) {
 			long newStartTime = getFileStartTime(getCurrentFile());
-			long diff = newStartTime - fileEndTime;
+			long diff = newStartTime - currFileEnd;
 			if (diff > 2000 || diff < -5000 || newStartTime == 0) {
 				currentFile--;
 				return false;

src/Filters/FilterControl.java

@@ -109,7 +109,12 @@ public class FilterControl extends PamControlledUnit implements PamSettings {
 	public void notifyModelChanged(int changeType) {
 		//System.out.println("FFTControl: notifyModelChanged : " +changeType);
 		super.notifyModelChanged(changeType);
-		if (filterGUIFX!=null) filterGUIFX.notifyGUIChange(changeType);
+		if (changeType == PamController.INITIALIZATION_COMPLETE) {
+			filterProcess.setupProcess();
+		}
+		if (filterGUIFX!=null) {
+			filterGUIFX.notifyGUIChange(changeType);
+		}
 	}
 	
 	public Serializable getSettingsReference() {

src/Filters/FilterProcess.java

@@ -75,8 +75,12 @@ public class FilterProcess extends PamProcess {
 		if (rawDataBlock == null) {
 			return;
 		}
+		boolean initComplete = PamController.getInstance().isInitializationComplete();
+		if (initComplete) {
+			int rawChannels = rawDataBlock.getChannelMap();
 			filterControl.filterParams.channelBitmap &= rawDataBlock.getChannelMap();
 			outputData.setChannelMap(filterControl.filterParams.channelBitmap);
+		}
 		int maxChan = PamUtils.getHighestChannel(filterControl.filterParams.channelBitmap);
 		iirfFilters = new Filter[maxChan+1];
 		FilterMethod filterMethod = FilterMethod.createFilterMethod(getSampleRate(), filterControl.filterParams.filterParams);

src/PamController/PamguardVersionInfo.java

@@ -31,7 +31,7 @@ public class PamguardVersionInfo {
 	 * Version number, major version.minorversion.sub-release.
 	 * Note: can't go higher than sub-release 'f'
 	 */
-	static public final String version = "2.02.03";
+	static public final String version = "2.02.03a";
 	
 	/**
 	 * Release date

src/annotation/userforms/datasel/UserFormDataSelCreator.java

@@ -10,6 +10,11 @@ import loggerForms.dataselect.FormDataSelCreator;
 import loggerForms.dataselect.FormDataSelector;
 import loggerForms.monitor.FormsDataSelectorCreator;
 
+/**
+ * User form data selector for use with annotations. Not normal selectors. 
+ * @author dg50
+ *
+ */
 public class UserFormDataSelCreator extends AnnotationDataSelCreator {
 
 	private FormDataSelCreator formsDataSelectorCreator;

src/gpl/GPLProcess.java

@@ -87,6 +87,7 @@ public class GPLProcess extends PamBlockProcess {
 		addOutputDataBlock(whitenedSpectrogram);
 		
 		stateDataBlock = new GPLStateDataBlock(this, 0);
+		stateDataBlock.setBinaryDataSource(new GPLStateDataSource(stateDataBlock));
 		addOutputDataBlock(stateDataBlock);
 		
 		gplDetectionBlock = new GPLDetectionBlock(this);
@@ -780,12 +781,13 @@ public class GPLProcess extends PamBlockProcess {
 
 
 			//			quiet.noise_floor = 1.;
+
+		}		
 		/**
 		 * This is the call to the detector, which is remembering state, will mostly return
 		 * null, but when there has been a detection, will return an object with time and 
 		 * frequency information. 
 		 */
-		}
 		public void runDetector(FFTDataUnit fftDataUnit, double[] wData, double base_in, double ceilnoise, double threshfloor) {		
 			//			DetectedPeak newPeak = peakDetector.detectPeaks(fftDataUnit, wData, base_in, 
 			//					gplParams.noise_ceiling * noise_floor, gplParams.thresh * noise_floor);		

src/gpl/GPLStateDataSource.java

@@ -0,0 +1,109 @@
+package gpl;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.IOException;
+
+import PamguardMVC.PamDataBlock;
+import PamguardMVC.PamDataUnit;
+import binaryFileStorage.BinaryDataSource;
+import binaryFileStorage.BinaryHeader;
+import binaryFileStorage.BinaryObjectData;
+import binaryFileStorage.ModuleFooter;
+import binaryFileStorage.ModuleHeader;
+
+public class GPLStateDataSource extends BinaryDataSource {
+
+	private GPLStateDataBlock gplStateDataBlock;
+	private ByteArrayOutputStream bos;
+	private DataOutputStream dos;
+	
+	public GPLStateDataSource(GPLStateDataBlock gplStateDataBlock) {
+		super(gplStateDataBlock);
+		this.gplStateDataBlock = gplStateDataBlock;
+	}
+
+	@Override
+	public String getStreamName() {
+		return "GPL State";
+	}
+
+	@Override
+	public int getStreamVersion() {
+		return 0;
+	}
+
+	@Override
+	public int getModuleVersion() {
+		return 0;
+	}
+
+	@Override
+	public byte[] getModuleHeaderData() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public PamDataUnit sinkData(BinaryObjectData binaryObjectData, BinaryHeader bh, int moduleVersion) {
+		DataInputStream dis = new DataInputStream(new ByteArrayInputStream(binaryObjectData.getData()));
+		try {
+			double baseline = dis.readFloat();
+			double ceilnoise = dis.readFloat();
+			double threshfloor = dis.readFloat();;
+			int state = dis.readShort();
+			GPLStateDataUnit stateData = new GPLStateDataUnit(binaryObjectData.getDataUnitBaseData(), baseline, ceilnoise, threshfloor, state);
+			return stateData;
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		
+		return null;
+	}
+
+	@Override
+	public ModuleHeader sinkModuleHeader(BinaryObjectData binaryObjectData, BinaryHeader bh) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public ModuleFooter sinkModuleFooter(BinaryObjectData binaryObjectData, BinaryHeader bh,
+			ModuleHeader moduleHeader) {
+		return null;
+	}
+
+	@Override
+	public BinaryObjectData getPackedData(PamDataUnit pamDataUnit) {
+		if (bos == null) {
+			bos = new ByteArrayOutputStream(14);
+			dos = new DataOutputStream(bos);
+		}
+		else {
+			bos.reset();
+		}
+		GPLStateDataUnit stateData = (GPLStateDataUnit) pamDataUnit;
+		try {
+			dos.writeFloat((float) stateData.getBaseline());
+			dos.writeFloat((float) stateData.getCeilnoise());
+			dos.writeFloat((float) stateData.getThreshfloor());
+			dos.writeShort((short) stateData.getPeakState());
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+				
+		BinaryObjectData bod = new BinaryObjectData(1, bos.toByteArray());
+		
+		return bod;
+	}
+
+	@Override
+	public void newFileOpened(File outputFile) {
+		// TODO Auto-generated method stub
+
+	}
+
+}

src/gpl/GPLStateDataUnit.java

@@ -1,5 +1,6 @@
 package gpl;
 
+import PamguardMVC.DataUnitBaseData;
 import PamguardMVC.PamDataUnit;
 
 public class GPLStateDataUnit extends PamDataUnit {
@@ -30,6 +31,23 @@ public class GPLStateDataUnit extends PamDataUnit {
 		this.threshfloor = threshfloor;
 	}
 	
+	/**
+	 * constructor used reading back from binary files. 
+	 * @param baseData
+	 * @param baseline
+	 * @param ceilnoise
+	 * @param threshfloor
+	 * @param peakState
+	 */
+	public GPLStateDataUnit(DataUnitBaseData baseData,double baseline, 
+			double ceilnoise, double threshfloor, int peakState) {
+		super(baseData);
+		this.baseline = baseline;
+		this.peakState = peakState;
+		this.ceilnoise = ceilnoise;
+		this.threshfloor = threshfloor;
+	}
+	
 	/**
 	 * @return the ceilnoise
 	 */

src/loggerForms/FormPlotOptions.java

@@ -44,7 +44,7 @@ public class FormPlotOptions implements Serializable, Cloneable, ManagedParamete
 	 */
 	public boolean isPlotControl(int controlIndex, int itemIndex) {
 		checkDimension(controlIndex, itemIndex);
-		return controlChoices[controlIndex][itemIndex];
+		return controlChoices[controlIndex][itemIndex] | true;
 	}
 	
 	/**

src/loggerForms/FormsDataBlock.java

@@ -4,6 +4,10 @@ import PamController.PamController;
 import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamProcess;
+import PamguardMVC.dataSelector.DataSelector;
+import PamguardMVC.dataSelector.DataSelectorCreator;
+import loggerForms.dataselect.FormDataSelCreator;
+import loggerForms.monitor.FormsDataSelectorCreator;
 /**
  * 
  * @author Graham Weatherup
@@ -18,6 +22,7 @@ public class FormsDataBlock extends PamDataBlock<FormsDataUnit> {
 		super(FormsDataUnit.class, dataName, parentProcess, channelMap);
 		this.formDescription = formDescription;
 		setNaturalLifetime(600);
+		setDataSelectCreator(new FormDataSelCreator(this, formDescription));
 //		setBinaryDataSource(new FormsBinaryIO(formDescription.getFormsControl(), this));
 //		setNaturalLifetimeMillis(60000);
 	}
@@ -26,6 +31,18 @@ public class FormsDataBlock extends PamDataBlock<FormsDataUnit> {
 		return formDescription;
 	}
 	
+//	@Override
+//	public DataSelector getDataSelector(String selectorName, boolean allowScores, String selectorType) {
+//		// TODO Auto-generated method stub
+//		return super.getDataSelector(selectorName, allowScores, selectorType);
+//	}
+//
+//	@Override
+//	public DataSelectorCreator getDataSelectCreator() {
+//
+//		dataSelectorCreator = new FormDataSelCreator(this, formDescription);
+//	}
+
 	/**
 	 * Override this for Logger forms so that they always save.
 	 * @param pamDataUnit dataunit to consider

src/loggerForms/FormsDataUnit.java

@@ -1,5 +1,6 @@
 package loggerForms;
 
+import GPS.GpsData;
 import PamUtils.PamCalendar;
 import PamguardMVC.PamDataUnit;
 /**
@@ -28,6 +29,8 @@ public class FormsDataUnit extends PamDataUnit {
 	private Object[] formData;
 	private FormDescription formDescription;
 
+	private GpsData formOriginLatLong;
+	
 	/**
 	 * Constructor for a form data unit. 
 	 * @param loggerForm
@@ -72,5 +75,23 @@ public class FormsDataUnit extends PamDataUnit {
 		this.updateDataUnit(PamCalendar.getTimeInMillis());
 	}
 
+	@Override
+	public GpsData getOriginLatLong(boolean recalculate) {
+		/**
+		 * Need to do something a bit different here since Logger form data is generally 
+		 * not associated with a hydrophone (though that may change in the future). 
+		 * All we really want is the primary origin method, which is either GPS data 
+		 * or static data and then get the value. mostly people will want the GPS position 
+		 * for the time of the logger data, though really we should make a much better way 
+		 * of doing this, including offsets from GPS, options to use the hydrophones if 
+		 * we want to as a reference, etc. 
+		 */
+		if (recalculate || formOriginLatLong == null) {
+			formOriginLatLong = loggerForm.getOriginLatLong(this);
+		}
+		return formOriginLatLong;
+	}
+
+
 
 }

src/loggerForms/LoggerForm.java

@@ -25,6 +25,12 @@ import javax.swing.JRootPane;
 import javax.swing.JScrollPane;
 import javax.swing.Timer;
 
+import Array.streamerOrigin.GPSOriginMethod;
+import Array.streamerOrigin.GPSOriginSystem;
+import Array.streamerOrigin.HydrophoneOriginMethod;
+import Array.streamerOrigin.HydrophoneOriginMethods;
+import Array.streamerOrigin.OriginIterator;
+import Array.streamerOrigin.StaticOriginSystem;
 import loggerForms.PropertyTypes;
 import loggerForms.controlDescriptions.ControlDescription;
 import loggerForms.controlDescriptions.ControlTypes;
@@ -33,6 +39,7 @@ import loggerForms.controls.CounterControl;
 import loggerForms.controls.LoggerControl;
 import loggerForms.controls.NMEAControl;
 import GPS.GPSDataBlock;
+import GPS.GpsData;
 import GPS.GpsDataUnit;
 import NMEA.NMEADataBlock;
 import NMEA.NMEADataUnit;
@@ -44,6 +51,7 @@ import PamView.dialog.PamDialog;
 import PamView.dialog.PamLabel;
 import PamView.panel.PamPanel;
 import PamView.panel.VerticalLayout;
+import PamguardMVC.PamDataBlock;
 import PamguardMVC.PamDataUnit;
 import PamguardMVC.PamObservable;
 import PamguardMVC.PamObserver;
@@ -94,6 +102,10 @@ public class LoggerForm{
 
 	private boolean hasCounter=false;
 	private CounterControl counter;
+	
+
+	private HydrophoneOriginMethods origins = HydrophoneOriginMethods.getInstance();
+	
 	/**
 	 * @return the hasCounter
 	 */
@@ -899,6 +911,32 @@ public class LoggerForm{
 		return saveButton;
 	}
 	
+	public GpsData getOriginLatLong(FormsDataUnit formsDataUnit) {
+		GpsData gps = getOrigin(GPSOriginSystem.class, formsDataUnit);
+		if (gps != null) {
+			return gps;
+		}
+		gps = getOrigin(StaticOriginSystem.class, formsDataUnit);
+		return gps;
+	}
+	
+	private GpsData getOrigin(Class originClass, FormsDataUnit formsDataUnit) {
+		HydrophoneOriginMethod origin = origins.getMethod(GPSOriginMethod.class, null, null);
+		if (origin == null) {
+			return null;
+		}
+		OriginIterator gpsIter = origin.getGpsDataIterator(PamDataBlock.ITERATOR_END);
+		GpsData prev = null;
+		while (gpsIter.hasPrevious()) {
+			prev = gpsIter.previous();
+			if (prev.getTimeInMillis() < formsDataUnit.getTimeMilliseconds()) {
+				break;
+			}
+		}
+		return prev;		
+	}
+	
+
 	//	/**
 	//	 * @return formsDataUnit
 	//	 */